# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:10:51 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 4-methoxy-~{N}-oxidanyl-3-(2-phenylethanoylamino)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1NC(=O)Cc2ccccc2)C(=O)NO
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 GRK  GRK  4-methoxy-~{N}-oxidanyl-3-(2-phenylethanoylamino)benzamide  ligand  38  22  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GRK
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 GRK  C8   C  CR6   0   0.342   2.0253  -1.9583   0.0129
 GRK  C5   C  CR6   0  -0.059   2.9527   0.6409  -0.3493
 GRK  C6   C  CR16  0  -0.288   3.8500  -0.4069  -0.2140
 GRK  C10  C  CR16  0  -0.347   1.5799   0.3871  -0.3200
 GRK  C12  C  CH3   0  -0.435   2.3345  -4.2932   0.3520
 GRK  C14  C  C     0   0.561  -1.3442  -0.4570  -0.2264
 GRK  C16  C  CH2   0  -0.705  -2.6490  -1.2291  -0.1073
 GRK  C17  C  CR6   0   0.156  -3.8420  -0.3262  -0.0223
 GRK  C18  C  CR16  0  -0.297  -4.2629   0.1747   1.2065
 GRK  C19  C  CR16  0  -0.242  -5.3596   1.0213   1.2889
 GRK  C20  C  CR16  0  -0.269  -6.0512   1.3799   0.1388
 GRK  C21  C  CR16  0  -0.243  -5.6389   0.8850  -1.0914
 GRK  C22  C  CR16  0  -0.305  -4.5401   0.0393  -1.1687
 GRK  C3   C  C     0   0.492   3.3879   2.0467  -0.5800
 GRK  C7   C  CR16  0  -0.371   3.3862  -1.7037  -0.0354
 GRK  C9   C  CR6   0   0.305   1.1008  -0.8982  -0.1275
 GRK  N13  N  NH1   0  -0.743  -0.2500  -1.2423  -0.0547
 GRK  N2   N  NH1   0  -0.378   4.5525   2.3664   0.0125
 GRK  O1   O  OH1   0  -0.540   5.1332   3.5745  -0.2102
 GRK  O11  O  O2    0  -0.478   1.4829  -3.1737   0.1842
 GRK  O15  O  O     0  -0.453  -1.3040   0.7335  -0.4669
 GRK  O4   O  O     0  -0.473   2.7326   2.8396  -1.2369
 GRK  H1   H  HCR6  0   0.267   4.9188  -0.2474  -0.2706
 GRK  H2   H  HCR6  0   0.287   0.8891   1.2058  -0.4350
 GRK  H3   H  HCH3  0   0.236   2.9709  -4.4486  -0.5217
 GRK  H4   H  HCH3  0   0.237   2.9622  -4.1913   1.2399
 GRK  H5   H  HCH3  0   0.267   1.6854  -5.1559   0.4738
 GRK  H6   H  HCH2  0   0.305  -2.7266  -1.8845  -0.9805
 GRK  H7   H  HCH2  0   0.294  -2.6020  -1.8897   0.7622
 GRK  H8   H  HCR6  0   0.250  -3.7317  -0.1031   2.1097
 GRK  H9   H  HCR6  0   0.255  -5.6756   1.3992   2.2527
 GRK  H10  H  HCR6  0   0.255  -6.9086   2.0373   0.2015
 GRK  H11  H  HCR6  0   0.255  -6.1744   1.1552  -1.9925
 GRK  H12  H  HCR6  0   0.250  -4.2263  -0.3449  -2.1322
 GRK  H13  H  HCR6  0   0.292   4.1049  -2.5062   0.0529
 GRK  H14  H  HNH1  0   0.421  -0.4311  -2.2158   0.1398
 GRK  H15  H  HNH1  0   0.421   5.0362   1.7645   0.6621
 GRK  H16  H  HOH1  0   0.477   4.7447   4.1908   0.4257

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 GRK  C12  O11  single    1.417  0.020  1.417
 GRK  C7   C6   aromatic  1.389  0.020  1.389
 GRK  C7   C8   aromatic  1.385  0.020  1.385
 GRK  C6   C5   aromatic  1.386  0.020  1.386
 GRK  O11  C8   single    1.342  0.020  1.342
 GRK  C8   C9   aromatic  1.414  0.020  1.414
 GRK  N2   O1   single    1.359  0.020  1.359
 GRK  N2   C3   single    1.345  0.020  1.345
 GRK  C5   C3   single    1.490  0.020  1.490
 GRK  C5   C10  aromatic  1.396  0.020  1.396
 GRK  C9   C10  aromatic  1.385  0.020  1.385
 GRK  C9   N13  single    1.396  0.020  1.396
 GRK  C3   O4   double    1.220  0.020  1.220
 GRK  N13  C14  single    1.358  0.020  1.358
 GRK  O15  C14  double    1.215  0.020  1.215
 GRK  C14  C16  single    1.521  0.020  1.521
 GRK  C16  C17  single    1.499  0.020  1.499
 GRK  C18  C17  aromatic  1.392  0.020  1.392
 GRK  C18  C19  aromatic  1.388  0.020  1.388
 GRK  C17  C22  aromatic  1.391  0.020  1.391
 GRK  C19  C20  aromatic  1.389  0.020  1.389
 GRK  C22  C21  aromatic  1.389  0.020  1.389
 GRK  C20  C21  aromatic  1.389  0.020  1.389
 GRK  C6   H1   single    0.930  0.020  1.080
 GRK  C10  H2   single    0.930  0.020  1.080
 GRK  C12  H3   single    0.970  0.020  1.090
 GRK  C12  H4   single    0.970  0.020  1.090
 GRK  C12  H5   single    0.970  0.020  1.090
 GRK  C16  H6   single    0.970  0.020  1.090
 GRK  C16  H7   single    0.970  0.020  1.090
 GRK  C18  H8   single    0.930  0.020  1.080
 GRK  C19  H9   single    0.930  0.020  1.080
 GRK  C20  H10  single    0.930  0.020  1.080
 GRK  C21  H11  single    0.930  0.020  1.080
 GRK  C22  H12  single    0.930  0.020  1.080
 GRK  C7   H13  single    0.930  0.020  1.080
 GRK  N13  H14  single    0.860  0.020  1.020
 GRK  N2   H15  single    0.860  0.020  1.020
 GRK  O1   H16  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 GRK  O11  C8   C9   115.31  3.000
 GRK  C9   C8   C7   120.08  3.000
 GRK  O11  C8   C7   124.61  3.000
 GRK  C3   C5   C10  117.52  3.000
 GRK  C10  C5   C6   119.80  3.000
 GRK  C3   C5   C6   122.64  3.000
 GRK  H1   C6   C7   118.31  3.000
 GRK  H1   C6   C5   121.52  3.000
 GRK  C7   C6   C5   120.15  3.000
 GRK  H2   C10  C9   119.88  3.000
 GRK  H2   C10  C5   119.34  3.000
 GRK  C9   C10  C5   120.77  3.000
 GRK  H5   C12  H4   109.04  3.000
 GRK  H5   C12  H3   108.96  3.000
 GRK  H4   C12  H3   109.19  3.000
 GRK  H5   C12  O11  106.36  3.000
 GRK  H4   C12  O11  111.59  3.000
 GRK  H3   C12  O11  111.60  3.000
 GRK  O15  C14  N13  124.40  3.000
 GRK  O15  C14  C16  122.77  3.000
 GRK  N13  C14  C16  112.82  3.000
 GRK  H7   C16  H6   106.01  3.000
 GRK  H7   C16  C17  110.68  3.000
 GRK  H6   C16  C17  110.46  3.000
 GRK  H7   C16  C14  109.40  3.000
 GRK  H6   C16  C14  107.60  3.000
 GRK  C17  C16  C14  112.43  3.000
 GRK  C22  C17  C18  118.76  3.000
 GRK  C22  C17  C16  120.73  3.000
 GRK  C18  C17  C16  120.50  3.000
 GRK  H8   C18  C19  119.61  3.000
 GRK  H8   C18  C17  119.68  3.000
 GRK  C19  C18  C17  120.71  3.000
 GRK  H9   C19  C20  120.12  3.000
 GRK  H9   C19  C18  119.77  3.000
 GRK  C20  C19  C18  120.12  3.000
 GRK  H10  C20  C21  120.20  3.000
 GRK  H10  C20  C19  120.22  3.000
 GRK  C21  C20  C19  119.58  3.000
 GRK  H11  C21  C22  119.80  3.000
 GRK  H11  C21  C20  120.11  3.000
 GRK  C22  C21  C20  120.09  3.000
 GRK  H12  C22  C21  119.64  3.000
 GRK  H12  C22  C17  119.62  3.000
 GRK  C21  C22  C17  120.74  3.000
 GRK  O4   C3   N2   123.19  3.000
 GRK  O4   C3   C5   122.66  3.000
 GRK  N2   C3   C5   114.14  3.000
 GRK  H13  C7   C6   118.80  3.000
 GRK  H13  C7   C8   120.92  3.000
 GRK  C6   C7   C8   120.28  3.000
 GRK  N13  C9   C10  124.80  3.000
 GRK  N13  C9   C8   116.28  3.000
 GRK  C10  C9   C8   118.91  3.000
 GRK  H14  N13  C9   114.93  3.000
 GRK  H14  N13  C14  115.96  3.000
 GRK  C9   N13  C14  129.10  3.000
 GRK  H15  N2   O1   115.53  3.000
 GRK  H15  N2   C3   123.84  3.000
 GRK  O1   N2   C3   120.60  3.000
 GRK  H16  O1   N2   106.69  3.000
 GRK  C12  O11  C8   119.21  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 GRK  CONST_01  C5   C6   C7   C8     0.00   0.0  0
 GRK  CONST_02  C5   C10  C9   C8     0.00   0.0  0
 GRK  CONST_03  C9   C8   C7   C6     0.00   0.0  0
 GRK  CONST_04  C9   C10  C5   C6     0.00   0.0  0
 GRK  CONST_05  C7   C6   C5   C10    0.00   0.0  0
 GRK  CONST_06  C7   C8   C9   C10    0.00   0.0  0
 GRK  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 GRK  CONST_08  C20  C21  C22  C17    0.00   0.0  0
 GRK  CONST_09  C21  C22  C17  C18    0.00   0.0  0
 GRK  CONST_10  C21  C20  C19  C18    0.00   0.0  0
 GRK  CONST_11  C22  C17  C18  C19    0.00   0.0  0
 GRK  CONST_12  C22  C21  C20  C19    0.00   0.0  0
 GRK  CONST_13  N13  C9   C10  C5   180.00   0.0  0
 GRK  CONST_14  O11  C8   C7   C6   180.00   0.0  0
 GRK  CONST_15  O11  C8   C9   C10  180.00   0.0  0
 GRK  CONST_16  C19  C18  C17  C16  180.00   0.0  0
 GRK  CONST_17  C21  C22  C17  C16  180.00   0.0  0
 GRK  CONST_18  C7   C6   C5   C3   180.00   0.0  0
 GRK  CONST_19  C9   C10  C5   C3   180.00   0.0  0
 GRK  CONST_20  N13  C9   C8   C7   180.00   0.0  0
 GRK  CONST_21  H1   C6   C7   C8   180.00   0.0  0
 GRK  CONST_22  H2   C10  C9   C8   180.00   0.0  0
 GRK  CONST_23  H13  C7   C6   C5   180.00   0.0  0
 GRK  CONST_24  H9   C19  C18  C17  180.00   0.0  0
 GRK  CONST_25  H11  C21  C22  C17  180.00   0.0  0
 GRK  CONST_26  H12  C22  C17  C18  180.00   0.0  0
 GRK  CONST_27  H10  C20  C19  C18  180.00   0.0  0
 GRK  CONST_28  H8   C18  C19  C20  180.00   0.0  0
 GRK  CONST_29  C14  N13  C9   C8   180.00   0.0  0
 GRK  CONST_30  C14  N13  C9   C10    0.00   0.0  0
 GRK  CONST_31  H14  N13  C9   C8     0.00   0.0  0
 GRK  CONST_32  O1   N2   C3   C5   180.00   0.0  0
 GRK  CONST_33  C9   N13  C14  C16  180.00   0.0  0
 GRK  CONST_34  O15  C14  N13  C9     0.00   0.0  0
 GRK  CONST_35  H15  N2   C3   C5     0.00   0.0  0
 GRK  CONST_36  O4   C3   N2   O1     0.00   0.0  0
 GRK  Var_01    N2   C3   C5   C6   -33.00  30.0  2
 GRK  Var_02    C7   C8   O11  C12    1.07  30.0  2
 GRK  Var_03    C18  C17  C16  C14  -86.55  30.0  2
 GRK  Var_04    N13  C14  C16  C17  168.50  30.0  1
 GRK  Var_05    H3   C12  O11  C8   -61.41  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 GRK  plan-1  C16  0.020
 GRK  plan-1  C17  0.020
 GRK  plan-1  C18  0.020
 GRK  plan-1  C19  0.020
 GRK  plan-1  C20  0.020
 GRK  plan-1  C21  0.020
 GRK  plan-1  C22  0.020
 GRK  plan-1  H8   0.020
 GRK  plan-1  H9   0.020
 GRK  plan-1  H10  0.020
 GRK  plan-1  H11  0.020
 GRK  plan-1  H12  0.020
 GRK  plan-2  C8   0.020
 GRK  plan-2  C5   0.020
 GRK  plan-2  C6   0.020
 GRK  plan-2  C10  0.020
 GRK  plan-2  C3   0.020
 GRK  plan-2  C7   0.020
 GRK  plan-2  C9   0.020
 GRK  plan-2  N13  0.020
 GRK  plan-2  O11  0.020
 GRK  plan-2  H1   0.020
 GRK  plan-2  H2   0.020
 GRK  plan-2  H13  0.020
 GRK  plan-3  C14  0.020
 GRK  plan-3  C16  0.020
 GRK  plan-3  C9   0.020
 GRK  plan-3  N13  0.020
 GRK  plan-3  O15  0.020
 GRK  plan-3  H14  0.020
 GRK  plan-4  C5   0.020
 GRK  plan-4  C3   0.020
 GRK  plan-4  N2   0.020
 GRK  plan-4  O1   0.020
 GRK  plan-4  O4   0.020
 GRK  plan-4  H15  0.020

